Rv: Value 99999999.9999 during minimization

From: Eduardo Tejera (edutp00_at_yahoo.com)
Date: Fri Aug 08 2008 - 14:50:45 CDT

Hi Rebeca   I had the same problem and was associated with 2 things: an error in the structure (the terminal residues) and a wrong dimension of Periodic Boundary Conditions. Maybe yo wish to inspect these aspect and try again.   Best Eduardo ----- Mensaje original ---- De: Schreiner Eduard <eschrein_at_ks.uiuc.edu> Para: rebeca_at_mmb.pcb.ub.es CC: namd-l_at_ks.uiuc.edu Enviado: viernes, 8 de agosto, 2008 9:44:12 Asunto: Re: namd-l: Value 99999999.9999 during minimization Hi Rebeca, without knowing any details of your system and simulation parameters, it looks like your structure has some clashes.  Maybe you wish to  inspect your system for atoms being too close to each other. As the piece of the output you posted shows, the large number is  showing you the van der Waals energy. But also the bond and the electrostatic  energies don't look good. If the minimization proceeds, monitor the corresponding energies and  check the structure after the minimization to take care that all the clashes are resolved  without introducing odd conformations. eddi On Aug 8, 2008, at 3:16 AM, rebeca_at_mmb.pcb.ub.es wrote: > Hello, > I am trying to do a simulation of a protein+membrane using NAMD/amber. > During the minimization, I am getting this: > > ETITLE:      TS          BOND          ANGLE          > DIHED          IMPRP >          ELECT            VDW      BOUNDARY          MISC        > KINETIC >        TOTAL          TEMP        TOTAL2        TOTAL3        > TEMPAVG > > ENERGY:      0  1703673.3943    136805.9022      > 47196.3199        0.0000 >  13846442.4891  99999999.9999        0.0000        0.0000          > 0.0000 > 99999999.9999        0.0000  99999999.9999  99999999.9999          > 0.0000 > > INITIAL STEP: 1e-06 > GRADIENT TOLERANCE: 1.40746e+06 > ENERGY:      1  1693389.9816    136708.8717      > 47190.9673        0.0000 >  13848767.3731  99999999.9999        0.0000        0.0000          > 0.0000 > 99999999.9999        0.0000  99999999.9999  99999999.9999          > 0.0000 > > ENERGY:      2  1683142.4203    136611.9751      > 47185.6190        0.0000 >  13851346.3909  99999999.9999        0.0000        0.0000          > 0.0000 > 99999999.9999        0.0000  99999999.9999  99999999.9999          > 0.0000 > > ENERGY:      3  1662754.8392    136418.5850      > 47174.9349        0.0000 >  13873293.1402  99999999.9999        0.0000        0.0000          > 0.0000 > 99999999.9999        0.0000  99999999.9999  99999999.9999          > 0.0000 > > (...) > > > I am a bit worried about the number 99999999.9999. I have more than  > 800,000 > atoms. Could this be a problem? > > Thank you very much for your help. > > Best wishes, > > Rebeca García Fandiño > Parc Cientific de Barcelona > rebeca_at_mmb.pcb.ub.es > > ===================================================== Eduard Schreiner Theoretical and Computational Biophysics Group NIH Resource for Macromolecular Modeling and Bioinformatics Beckman Institute for Advanced Science and Technology University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801 Phone: 217-244-4361 Fax: 217-244-6078 http://www.ks.uiuc.edu/~eschrein/ ============================================= ________________________________ Yahoo! MTV Blog & Rock ¡Cuéntanos tu historia, inspira una canción y gánate un viaje a los Premios MTV! Participa aquí http://mtvla.yahoo.com/ ____________________________________________________________________________________ Yahoo! MTV Blog & Rock &gt;¡Cuéntanos tu historia, inspira una canción y gánate un viaje a los Premios MTV! Participa aquí http://mtvla.yahoo.com/

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